GenomeDescription objects
A GenomeDescription object holds the meta information describing a given genome.
Even though a constructor function is provided (GenomeDescription()),
it is rarely needed
GenomeDescription objects are typically obtained by coercing a
BSgenome object to GenomeDescription. This has the
effect of stripping the sequences from the object and retaining only
the meta information that describes the genome. See the Examples section
below for an example.
In the code snippets below, object or x is a
GenomeDescription object.
organism(object):
Return the scientific name of the organism of the genome e.g.
"Homo sapiens", "Mus musculus",
"Caenorhabditis elegans", etc...
commonName(object):
Return the common name of the organism of the genome e.g.
"Human", "Mouse", "Worm", etc...
providerVersion(x):
Return the name of the genome. This is typically the name of an
NCBI assembly (e.g. GRCh38.p12, WBcel235, TAIR10.1,
ARS-UCD1.2, etc...) or UCSC genome (e.g. hg38,
bosTau9, galGal6, ce11, etc...).
provider(x):
Return the provider of this genome e.g. "UCSC", "BDGP",
"FlyBase", etc...
releaseDate(x):
Return the release date of this genome e.g. "Mar. 2006".
releaseName(x):
IMPORTANT NOTE: The releaseName() methods for GenomeDescription
and BSgenome objects are deprecated in BioC 3.12!
If x is a GenomeDescription object, releaseName(x)
returns the release name of this genome, which is usually made
of the name of the organization who assembled it plus its Build
version. For example, UCSC uses "hg18" for the version of
the Human genome corresponding to the Build 36.1 from NCBI hence
the release name for this genome is "NCBI Build 36.1".
If x is a BSgenome object, releaseName(x)
returns NA_character_.
bsgenomeName(x):
Uses the meta information stored in GenomeDescription object x
to construct the name of the corresponding BSgenome data package (see
the available.genomes function in the
BSgenome package for details about the naming scheme used
for those packages). Note that there is no guarantee that a package
with that name actually exists.
seqinfo(x)Gets information about the genome sequences. This information
is returned in a Seqinfo object.
Each part of the information can be retrieved separately with
seqnames(x), seqlengths(x), and isCircular(x),
respectively, as described below.
seqnames(x)Gets the names of the genome sequences.
seqnames(x) is equivalent to seqnames(seqinfo(x)).
seqlengths(x)Gets the lengths of the genome sequences.
seqlengths(x) is equivalent to seqlengths(seqinfo(x)).
isCircular(x)Returns the circularity flags of the genome sequences.
isCircular(x) is equivalent to isCircular(seqinfo(x)).
H. Pagès
The available.genomes function and the
BSgenome class in the BSgenome package.
The Seqinfo class.
library(BSgenome.Celegans.UCSC.ce2) BSgenome.Celegans.UCSC.ce2 as(BSgenome.Celegans.UCSC.ce2, "GenomeDescription")
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.